QC Measures

Low correlation!

Spearman correlation across replicates is low using a barcode threshold per oligo of 5! Spearman correlation of DNA is 0.29, RNA is 0.58 and DNA/RNA ratio is 0.52. Minimum allowed values are 0.85, 0.95, and 0.75.

Oligo Coorelatioin

Oligo correlation plots of DNA, RNA and DNA/RNA ratios across replicates. First tab shows plots using (in average) 1567 oligos with a minimum number of 5 barcodes. Second tab shows all 2016 oligos that have assigned barcodes.

Condition A B #Oligos A #Oligos B #Oligos Joined DNA spearman RNA spearman Ratio spearman DNA log2 pearson RNA log2 pearson Ratio log2 pearson
HepG2 1 2 1662 1684 1564 0.33 0.60 0.53 0.32 0.70 0.62
HepG2 1 3 1662 1700 1556 0.29 0.61 0.55 0.28 0.71 0.63
HepG2 2 3 1684 1700 1582 0.31 0.58 0.52 0.31 0.68 0.62
Condition A B #Oligos A #Oligos B #Oligos Joined DNA spearman RNA spearman Ratio spearman DNA log2 pearson RNA log2 pearson Ratio log2 pearson
HepG2 1 2 2031 2028 2016 0.28 0.53 0.45 0.27 0.61 0.51
HepG2 1 3 2031 2030 2018 0.27 0.53 0.46 0.26 0.59 0.51
HepG2 2 3 2028 2030 2016 0.28 0.51 0.43 0.28 0.58 0.50

Experiment statistic

The total number of oligos in this experiment is 2050 (defined by the assignment) with 58369 associated barcodes.

In average across replicates we see 2030 from 25281 average barcodes in the count data and around 71255 barcodes where not in the assignment.

condition replicate oligos dna/rna matched barcodes unknown barcodes dna/rna % matched barcodes total dna counts total rna counts avg dna counts per bc avg rna counts per bc avg dna/rna barcodes per oligo
HepG2 1 2031 25038 71955 25.81 212037 566550 2.19 5.84 12.33
HepG2 2 2028 25420 71141 26.33 201559 564222 2.09 5.84 12.53
HepG2 3 2030 25384 70668 26.43 197109 601951 2.05 6.27 12.50
Experiment Barcodes Counts Average counts Assigned barcodes Assigned counts Average assigned counts Fraction assigned barcodes Fraction assigned counts
HepG2_1_DNA 149172 294136 1.97 32993 75057 2.27 0.22 0.26
HepG2_2_DNA 153364 289183 1.89 34261 74150 2.16 0.22 0.26
HepG2_3_DNA 152734 285380 1.87 34281 73508 2.14 0.22 0.26
HepG2_1_RNA 190654 871820 4.57 38356 229135 5.97 0.20 0.26
HepG2_2_RNA 187952 878332 4.67 38144 233350 6.12 0.20 0.27
HepG2_3_RNA 192812 959790 4.98 38566 253313 6.57 0.20 0.26

Number of barcodes per oligo

Histogramm of number of barcodes per oligo. Median is blue, mean is red.

Activity

Violin and box plots of the log2 fold change of all oligos by the assay. Grouped by labels if set, otherwise NA. First tab shows plots using (in average) 1567 oligos with a minimum number of 5 barcodes. Second tab shows all 2016 oligos that have assigned barcodes.